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Objectives <p>To present authors’ experience of chromosome microarray analysis (CMA) as the first-tier test, which contributed to accumulation and annotation of copy number variations (CNVs) and discovery of novel genetic hot spots in Indian pediatric patients.</p> Methods <p>Karyotyping and CMA (4X180K Agilent) were performed in 300 patients with developmental delay, dysmorphism, autism, intellectual disability or congenital malformations. Various databases such as ClinVar, Clin Gen, OMIM, DECIPHER, etc<i>.</i> were used for interpretation of the results.</p> Results <p>The diagnostic yield of clinically significant findings by CMA [16.00% (48/300)] was 9.0% higher than that by karyotyping [7.0% (21/300)]. There were 2.66% (08/300) patients with variations of uncertain significance (VOUS) which were challenging to interpret. Benign variations were considered normal.</p> Conclusions <p>CMA allows increased diagnostic yield of known and new microdeletion/duplication syndromes and molecular characterization of marker chromosomes with gene annotations. There is insufficient data published from India. Every such test done on Indian patients contributes to Indian data accumulation of pathogenic CNVs (pCNVs) and VOUS for future resolution. The benefit of CMA as a first-tier test is that it can improve the understanding towards the associated known and new genetic hot spots, thus providing a better genotype–phenotype correlation. Pre-test and post-test genetic counseling is important.</p>

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Diagnostic Yield of Chromosomal Microarray Analysis in a Cohort of 300 Indian Patients

  • 期刊论文

  • 发表日期：

    2025年5月8日

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  • Meena Bajaj Lall,
  • Anju Joshi,
  • Shruti Agarwal,
  • Pushpa Saviour,
  • Preeti Paliwal,
  • Sunita Bijarnia Mahay,
  • Ratna Dua Puri,
  • Ishwar Chander Verma

摘要

Objectives

To present authors’ experience of chromosome microarray analysis (CMA) as the first-tier test, which contributed to accumulation and annotation of copy number variations (CNVs) and discovery of novel genetic hot spots in Indian pediatric patients.

Methods

Karyotyping and CMA (4X180K Agilent) were performed in 300 patients with developmental delay, dysmorphism, autism, intellectual disability or congenital malformations. Various databases such as ClinVar, Clin Gen, OMIM, DECIPHER, etc. were used for interpretation of the results.

Results

The diagnostic yield of clinically significant findings by CMA [16.00% (48/300)] was 9.0% higher than that by karyotyping [7.0% (21/300)]. There were 2.66% (08/300) patients with variations of uncertain significance (VOUS) which were challenging to interpret. Benign variations were considered normal.

Conclusions

CMA allows increased diagnostic yield of known and new microdeletion/duplication syndromes and molecular characterization of marker chromosomes with gene annotations. There is insufficient data published from India. Every such test done on Indian patients contributes to Indian data accumulation of pathogenic CNVs (pCNVs) and VOUS for future resolution. The benefit of CMA as a first-tier test is that it can improve the understanding towards the associated known and new genetic hot spots, thus providing a better genotype–phenotype correlation. Pre-test and post-test genetic counseling is important.